From CSBLwiki

Contents 1 Pan-Genomic Universe 1.1 Data 1.2 Results 1.2.1 MDS 1.3 R script sources

Pan-Genomic Universe

Data

• Pan-Genome data version 0.1 Feb 2010
• Download the frequency profile (1,137 genomes x 11,912 pfam domains)
  • download: The FP(Frequency Profile) matrix

Results

MDS

• Procedures

1. build a pairwise distance matrix (11,912 x 11,912) from the FP matrix (1,137 x 11,912) - euclidean distance
2. do MDS (multidimensional scaling) of the distance matrix
3. get coordinates from the first three dimension and plot them in a 3D-space

• Exact distance matrix

R script sources